hictk - v2.1.4

What's Changed

This is a patch release consisting of one bugfix concerning the help message showing information regarding telemetry collection.

I also took the occasion to refactor the conanfile.py and improve the instructions to build hictk from source.

Changelog

• [fix]: hictk --help-telemetry by @robomics in https://github.com/paulsengroup/hictk/pull/422
• [refactor]: rewrite conanfile.py to be more modular by @robomics in https://github.com/paulsengroup/hictk/pull/424
• [docs]: update instruction on how to build hictk from sources by @robomics in https://github.com/paulsengroup/hictk/pull/423

Full Changelog: https://github.com/paulsengroup/hictk/compare/v2.1.3...v2.1.4

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Published by robomics 12 months ago

hictk - v2.1.3

What's Changed

This is a small release consisting of a couple of bugfixes and a few changes to address new warnings issued by GCC 15 and Clang 20.

Changelog

• [fix]: hictk load: respect --drop-unknown-chroms by @robomics in https://github.com/paulsengroup/hictk/pull/415
• [perf]: strip hictk binary when compiling in Release by @robomics in https://github.com/paulsengroup/hictk/pull/416
• [dependencies]: bump by @robomics and @dependabot in https://github.com/paulsengroup/hictk/pull/418 and https://github.com/paulsengroup/hictk/pull/419
• [docs]: improve paging of CLI help messages by @robomics in https://github.com/paulsengroup/hictk/pull/420

Full Changelog: https://github.com/paulsengroup/hictk/compare/v2.1.2...v2.1.3

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Published by robomics 12 months ago

hictk - v2.1.2

What's Changed

This is a small release consisting of one bugfix and various improvements to the documentation and error messages.

Changelog

Bugfix

• [bug]: address bug in ToDataFrame transformer when span=full and queries are cis and have unusual shapes by @robomics in https://github.com/paulsengroup/hictk/pull/406

Improvements

• [feature]: improve error message generated by hictk balance by @robomics in https://github.com/paulsengroup/hictk/pull/401
• [feature]: improve error messages generated when opening .hic files by @robomics in https://github.com/paulsengroup/hictk/pull/411

Documentation

• [docs]: update the documentation by @robomics in https://github.com/paulsengroup/hictk/pull/412

Various

• [ci]: make build-conan-deps-* workflows more reliable by @robomics in https://github.com/paulsengroup/hictk/pull/402
• [deps]: bump by @pre-commit-ci, @dependabot, and @robomics in https://github.com/paulsengroup/hictk/pull/326, https://github.com/paulsengroup/hictk/pull/405, https://github.com/paulsengroup/hictk/pull/407, https://github.com/paulsengroup/hictk/pull/410

Full Changelog: https://github.com/paulsengroup/hictk/compare/v2.1.1...v2.1.2

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Published by robomics about 1 year ago

hictk - v2.1.1

What's Changed

This release consists of a single minor bug fix.

• [bug]: fix segfault when fetching genome-wide interactions from empty .hic files by @robomics in https://github.com/paulsengroup/hictk/pull/399

Full Changelog: https://github.com/paulsengroup/hictk/compare/v2.1.0...v2.1.1

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Published by robomics about 1 year ago

hictk - v2.1.0

What's Changed

This release contains a mix of new features, performance improvements, and bug fixes.

Highlighted features

Fetching interactions around the matrix diagonal

We introduce a new transformer named DiagonalBand() which given a pair of pixel iterators, returns another pair of iterators that traverse pixels falling within a given matrix diagonal band. When DiagonalBand() is constructed from iterators coming from hictk's PixelSelectors, pixels are traversed as efficiently as possible by minimizing the number of pixels that are needlessly fetched from the files.

When using hictk::hic::Files, to achieve the best performance possible, be sure to specify the diagonal_band_width parameter when calling the fetch() method.

Improve performance of queries on Cooler files

With this release, we introduce a few heuristics to minimize the amount of unnecessary work that is performed when fetching interactions from Cooler files. This is especially noticeable when fetching interactions using "tall" queries (e.g. range1=chr1; range2=chrX:10,000,000-11,000,000). Overall, this resulted in an average performance improvement in the order of 20-40% (with up to 400% improvements in very specific cases, and a few minor regressions when fetching a very small number of interactions from small chromosomes). See https://github.com/paulsengroup/hictk/pull/330 for more details.

Quality of life improvements

• When opening .hic or .mcool files consisting of a single resolution using e.g. hictk::File(), the resolution parameter is no longer mandatory.
• The hictk CLI now supports common units for genomic distances. Example usage: hictk dump myfile.mcool --resolution 5Mbp (5Mb and 5M are equivalent to 5Mbp).
• Better error messages when attempting to open files with an invalid/missing resolution.

Telemetry

With this release, we introduce support for telemetry collection from the hictk CLI. We collect as little information as possible. More specifically we do NOT collect information that could be used to: - identify our users - identify the machine or environment where hictk is being run - know which dataset is being processed by hictk - the parameters used to run hictk

Telemetry collection can be disabled in a few ways, such as defining the HICTK_NO_TELEMETRY env variable before launching hictk.

Furthermore, we added a dedicated page to the documentation at hictk.readthedocs.io with detailed information regarding telemetry collection, processing, and storage. If you have any questions related to this topic, please start a new discussion on GitHub

Changelog

Changes to library code

• [perf]: improve performance of queries on Cooler files by @robomics in https://github.com/paulsengroup/hictk/pull/330
• [feature]: support efficient, lazy fetching of interactions falling within a diagonal band by @robomics in https://github.com/paulsengroup/hictk/pull/346
• [enhancement]: update ToDataFrame to use signed integers by @robomics in https://github.com/paulsengroup/hictk/pull/358
• [feature]: update transformers to dense/sparse matrices and dataframes to support fetching interactions surrounding the matrix diagonal by @robomics in https://github.com/paulsengroup/hictk/pull/356
• [feature]: implement avail_normalizations() on multi-resolution files by @robomics in https://github.com/paulsengroup/hictk/pull/362
• [feature]: improve automatic resolution inference by @robomics in https://github.com/paulsengroup/hictk/pull/368
• [enhancement]: improve error messages generated by hictk::File() by @robomics in https://github.com/paulsengroup/hictk/pull/377 and https://github.com/paulsengroup/hictk/pull/357
• [feature]: Support efficient computation of query size by @robomics in https://github.com/paulsengroup/hictk/pull/384
• [refactor]: improve layout of internal libs to better support partial builds by @robomics in https://github.com/paulsengroup/hictk/pull/397
• [build system]: make overriding git metadata embedding more flexible by @robomics in https://github.com/paulsengroup/hictk/pull/352
• [build system]: prefix internal CMake targets with hictk_ to avoid collisions for common names by @robomics in https://github.com/paulsengroup/hictk/pull/351

Changes to CLI tools

• [enhancement]: hictk convert: improve handling of files with normalizations not available across all resolutions by @robomics in https://github.com/paulsengroup/hictk/pull/365
• [feature]: update CLI to support common units for genomic distances by @robomics in https://github.com/paulsengroup/hictk/pull/369
• [perf] hictk validate: greatly improve performance when using --validate-index by @robomics in https://github.com/paulsengroup/hictk/pull/333
• [feature]: hictk validate: add CLI option to validate pixels from .[ms]cool files by @robomics in https://github.com/paulsengroup/hictk/pull/380
• [feature]: support creating .hic and .cool files with no interactions by @robomics in https://github.com/paulsengroup/hictk/pull/387
• [feature]: improve pixel validation when creating .cool/hic files by @robomics in https://github.com/paulsengroup/hictk/pull/388
• [feature]: make sure all well-behaved errors result in exit code 1 by @robomics in https://github.com/paulsengroup/hictk/pull/370
• [feature]: initial support for collecting telemetry by @robomics in https://github.com/paulsengroup/hictk/pull/372
• [fix]: hictk convert: do not hang when processing .cool files with pixels with 0 interactions by @robomics in https://github.com/paulsengroup/hictk/pull/379

Updates to CI

• [ci]: refactor by @robomics in https://github.com/paulsengroup/hictk/pull/340 and https://github.com/paulsengroup/hictk/pull/345
• [ci]: update fuzzy-testing.yml to collect coverage by @robomics in https://github.com/paulsengroup/hictk/pull/360
• [ci]: dependabot: reduce update frequency by @robomics in https://github.com/paulsengroup/hictk/pull/382
• [ci]: fix coverage reporting by @robomics in https://github.com/paulsengroup/hictk/pull/385
• [ci]: fix triggers for clang-tidy GHA workflow by @robomics in https://github.com/paulsengroup/hictk/pull/391
• [ci]: use LLD whenever possible by @robomics in https://github.com/paulsengroup/hictk/pull/393
• [ci]: fix build-conan-deps* workflows by @robomics in https://github.com/paulsengroup/hictk/pull/394
• [fix]: fix build-dockerfile.yml by @robomics in https://github.com/paulsengroup/hictk/pull/367
• [fix]: ensure ubuntu-ci.yml uses the generator specified through the job matrix by @robomics in https://github.com/paulsengroup/hictk/pull/376
• [pre-commit]: update config and add new hooks by @robomics in https://github.com/paulsengroup/hictk/pull/381

Updates to testing

• [fix]: address segfault in unit tests by @robomics in https://github.com/paulsengroup/hictk/pull/347
• [testing]: re-organize test datasets by @robomics in https://github.com/paulsengroup/hictk/pull/361
• [testing]: improve integration test suite by @robomics in https://github.com/paulsengroup/hictk/pull/363 and https://github.com/paulsengroup/hictk/pull/371
• [enhancement]: make utils/devel/testdockerimage.sh more generic by @robomics in https://github.com/paulsengroup/hictk/pull/375

Various

• [fix]: do not wrap string literals with FMTSTRING when using SPDLOG macros by @robomics in https://github.com/paulsengroup/hictk/pull/355
• [fix]: fix redirect of stdout to stderr in various scripts by @robomics in https://github.com/paulsengroup/hictk/pull/374
• [feature]: use CMake lock files when downloading or generating files by @robomics in https://github.com/paulsengroup/hictk/pull/350
• [docs]: Various updates and improvements by @robomics in https://github.com/paulsengroup/hictk/pull/353, https://github.com/paulsengroup/hictk/pull/390, https://github.com/paulsengroup/hictk/pull/392, and https://github.com/paulsengroup/hictk/pull/396
• [enhancement]: address clang-tidy warnings by @robomics in https://github.com/paulsengroup/hictk/pull/364 and https://github.com/paulsengroup/hictk/pull/366
• [deps]: bump by @robomics and @dependabot in https://github.com/paulsengroup/hictk/pull/389 and https://github.com/paulsengroup/hictk/pull/348

Full Changelog: https://github.com/paulsengroup/hictk/compare/v2.0.2...v2.1.0

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Published by robomics about 1 year ago

hictk - v2.0.2

What's Changed

This is a small maintenance release mostly consisting of bugfixes.

Bugfix

• Add missing include by @robomics in https://github.com/paulsengroup/hictk/pull/308
• [bug]: fix enum parsing in hictk CLI code by @robomics in https://github.com/paulsengroup/hictk/pull/332
• [bug]: fix mis-tagged unit tests by @robomics in https://github.com/paulsengroup/hictk/pull/335
• [bug]: fix handling of Cooler v2 files lacking the "storage-mode" attribute by @robomics in https://github.com/paulsengroup/hictk/pull/339

Various

• Improve throughput of float formatting by @robomics in https://github.com/paulsengroup/hictk/pull/311
• Address warnings when compiling project with C++23 by @robomics in https://github.com/paulsengroup/hictk/pull/310
• hictk: support replaying warnings right before app exit by @robomics in https://github.com/paulsengroup/hictk/pull/313
• Bump dependencies @dependabot, @pre-commit-ci and @robomics in in https://github.com/paulsengroup/hictk/pull/272, https://github.com/paulsengroup/hictk/pull/315, and https://github.com/paulsengroup/hictk/pull/317
• Updates to CI by @robomics in https://github.com/paulsengroup/hictk/pull/324, https://github.com/paulsengroup/hictk/pull/337, and https://github.com/paulsengroup/hictk/pull/338
• Update documentation by @robomics in https://github.com/paulsengroup/hictk/pull/316 and https://github.com/paulsengroup/hictk/pull/320
• [fix]: address warnings raised by CodeQL analysis by @robomics in https://github.com/paulsengroup/hictk/pull/319

New Contributors

• @pre-commit-ci made their first contribution in https://github.com/paulsengroup/hictk/pull/272

Full Changelog: https://github.com/paulsengroup/hictk/compare/v2.0.1...v2.0.2

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Published by robomics over 1 year ago

hictk - v2.0.1

The main motivation behind this release is to ensure that the up-to-date documentation is properly published on ReadTheDocs.

More details

hictk is relying on the linkcheck plugin to ensure that the documentation does not contain broken or invalid links. However, when the documentation is being built by the ReadTheDocs CI, some of the links in the docs are not yet valid (but they will be once the up-to-date documentation is published). linkcheck detected this issue and cancelled the CI job, which is why there is no documentation for hictk v2.0.0 on ReadTheDocs. PR https://github.com/paulsengroup/hictk/pull/299 updates linkcheck's ignore list such that the temporarily invalid links are not checked by linkcheck. The up-to-date documentation for hictk v2.0.1 is available at: [https://hictk.readthedocs.io/en/v2.0.1/](https://hictk.readthedocs.io/en/v2.0.1/)

What's Changed

• Update linkcheck ignore list by @robomics in https://github.com/paulsengroup/hictk/pull/299
• Remove unused workflow by @robomics in https://github.com/paulsengroup/hictk/pull/300
• Implement bins_ptr() accessor for cooler::SingleCellFile() by @robomics in https://github.com/paulsengroup/hictk/pull/298
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/301
• Fix typo in the README by @robomics in https://github.com/paulsengroup/hictk/pull/303

Full Changelog: https://github.com/paulsengroup/hictk/compare/v2.0.0...v2.0.1

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Published by robomics over 1 year ago

hictk - v2.0.0

What's Changed

• hictk published in Bioinformatics! by @robomics in https://github.com/paulsengroup/hictk/pull/194

Changes to library code

• Fix bug when fetching whole-genome interactions as dense or sparse matrix by @robomics in https://github.com/paulsengroup/hictk/pull/196, https://github.com/paulsengroup/hictk/pull/197
• Expose bin_ptr() accessor wherever it makes sense by @robomics in https://github.com/paulsengroup/hictk/pull/199
• Make hictk::common depend on the git-watcher target by @robomics in https://github.com/paulsengroup/hictk/pull/233
• Various improvements and bug fixes to code related to fetching interactions as Eigen matrices by @robomics in https://github.com/paulsengroup/hictk/pull/227
• Improve transformers::ToDataFrame() by @robomics in https://github.com/paulsengroup/hictk/pull/234
• Support merging streams of pixels originating from files of different formats by @robomics in https://github.com/paulsengroup/hictk/pull/243
• Fix division by zero when fetching pixels from coolers with bin tables with variable bin size by @robomics in https://github.com/paulsengroup/hictk/pull/250
• Various improvements to balancing::Weights by @robomics in https://github.com/paulsengroup/hictk/pull/251
• Fix bug when fetching normalized interactions as dense matrices by @robomics in https://github.com/paulsengroup/hictk/pull/252
• Minor changes to iterators by @robomics in https://github.com/paulsengroup/hictk/pull/253
• Improve support for "square" Cooler files by @robomics in https://github.com/paulsengroup/hictk/pull/249
• Rewrite VectorOfAtomicDecimals by @robomics in https://github.com/paulsengroup/hictk/pull/255
• Make constructors for To*Matrix transformers more flexible by @robomics in https://github.com/paulsengroup/hictk/pull/266
• Improve performance of ToSparseMatrix by reducing memory allocations by @robomics in https://github.com/paulsengroup/hictk/pull/277
• Refactor FileStream class by @robomics in https://github.com/paulsengroup/hictk/pull/282
• Replace HICTKUNREACHABLECODE macro with hictk::unreachable_code() by @robomics in https://github.com/paulsengroup/hictk/pull/285
• Make sure cooler::File::close() does not attempt to finalize files twice by @robomics in https://github.com/paulsengroup/hictk/pull/291
• Mark ~TmpDir() noexcept and log errors as warnings using spdlog by @robomics in https://github.com/paulsengroup/hictk/pull/292
• Improve logging when failures occur from within class destructors by @robomics in https://github.com/paulsengroup/hictk/pull/293
• Add option to exclude "ALL" chromosomes when calling nchroms() on .hic files by @robomics in https://github.com/paulsengroup/hictk/pull/294

Changes to CLI tools

• Better handling of coolers with FP counts by @robomics in https://github.com/paulsengroup/hictk/pull/201, https://github.com/paulsengroup/hictk/pull/202
• Implement hictk metadata command by @robomics in https://github.com/paulsengroup/hictk/pull/204, https://github.com/paulsengroup/hictk/pull/222
• Improve error message when temporary folder cannot be safely determined by @robomics in https://github.com/paulsengroup/hictk/pull/210
• Fix CLI exit code by @robomics in https://github.com/paulsengroup/hictk/pull/215
• Add --no-create-weight-link CLI flag where appropriate by @robomics in https://github.com/paulsengroup/hictk/pull/223
• Minor improvements to various hictk subcommands by @robomics in https://github.com/paulsengroup/hictk/pull/229, https://github.com/paulsengroup/hictk/pull/231, https://github.com/paulsengroup/hictk/pull/232, https://github.com/paulsengroup/hictk/pull/228, https://github.com/paulsengroup/hictk/pull/238
• Add option to override count type used to convert .hic files to .[m]cool format by @robomics in https://github.com/paulsengroup/hictk/pull/203
• hictk load: support ingesting interactions from pairs/pixel files with interactions overlapping with the lower-triangular matrix by @robomics in https://github.com/paulsengroup/hictk/pull/264
• Tweak max active log level based on CMake build type by @robomics in https://github.com/paulsengroup/hictk/pull/278
• Fix default log levels when compiling hictk in Debug mode by @robomics in https://github.com/paulsengroup/hictk/pull/279
• Ensure no temporary files are written when balancing .hic files with --in-memory by @robomics in https://github.com/paulsengroup/hictk/pull/280
• hictk load: support loading compressed interactions by @robomics in https://github.com/paulsengroup/hictk/pull/244
• Fix temporary file name collisions in hictk convert *cool -> hic by @robomics in https://github.com/paulsengroup/hictk/pull/274

Updates to CI

• Bump GH Actions by @dependabot in https://github.com/paulsengroup/hictk/pull/61, https://github.com/paulsengroup/hictk/pull/188
• Update .pre-commit-config.yaml by @robomics in https://github.com/paulsengroup/hictk/pull/198, https://github.com/paulsengroup/hictk/pull/270
• Use prettier to format MD and YAML files by @robomics in https://github.com/paulsengroup/hictk/pull/221
• Reduce duration of fuzzy test CI when triggered by PRs by @robomics in https://github.com/paulsengroup/hictk/pull/254
• Update cppstd.yml by @robomics in https://github.com/paulsengroup/hictk/pull/259
• Disable ccache in fuzzy-testing.yml by @robomics in https://github.com/paulsengroup/hictk/pull/260
• Optimize CI workflows by @robomics in https://github.com/paulsengroup/hictk/pull/268
• Add workflows to lint project by @robomics in https://github.com/paulsengroup/hictk/pull/269
• Use gersemi instead of cmake-format to format CMake files by @robomics in https://github.com/paulsengroup/hictk/pull/283
• Bump clang-tidy used by CI by @robomics in https://github.com/paulsengroup/hictk/pull/284
• Add macos-15 to CI test matrix by @robomics in https://github.com/paulsengroup/hictk/pull/287
• Fix ccache cache eviction logic when using GHA job matrix by @robomics in https://github.com/paulsengroup/hictk/pull/288
• Bump compiler used to build Dockerfile to clang-19 by @robomics in https://github.com/paulsengroup/hictk/pull/256

Updates to testing

• Add automated tests covering hictk's packaging by @robomics in https://github.com/paulsengroup/hictk/pull/246
• Rewrite hictk's fuzzer by @robomics in https://github.com/paulsengroup/hictk/pull/226
• Test compatibility with newer C++ standards by @robomics in https://github.com/paulsengroup/hictk/pull/258
• Overhaul of the integration test suite by @robomics in https://github.com/paulsengroup/hictk/pull/257
• Improve coverage by @robomics in https://github.com/paulsengroup/hictk/pull/263
• Increase integration test base timeout by @robomics in https://github.com/paulsengroup/hictk/pull/281
• Fix to fuzzer suite by @robomics in https://github.com/paulsengroup/hictk/pull/290
• Fix visibility warnings issued when compiling hictk_fuzzer using GCC by @robomics in https://github.com/paulsengroup/hictk/pull/276

Various

• Allow dynamically linking to Arrow libs even when building with static linking by @robomics in https://github.com/paulsengroup/hictk/pull/200
• Reduce size of hictk's Docker image by @robomics in https://github.com/paulsengroup/hictk/pull/209
• Update docs by @robomics in https://github.com/paulsengroup/hictk/pull/195, https://github.com/paulsengroup/hictk/pull/208
• Refactor by @robomics in https://github.com/paulsengroup/hictk/pull/245
• Add missing dep in conanfile.py by @robomics in https://github.com/paulsengroup/hictk/pull/265
• Improve compilation times by @robomics in https://github.com/paulsengroup/hictk/pull/262
• Fix SPDX headers by @robomics in https://github.com/paulsengroup/hictk/pull/267
• Fix Release builds on GCC8 by @robomics in https://github.com/paulsengroup/hictk/pull/273
• Bump dependencies by @robomics in https://github.com/paulsengroup/hictk/pull/247
• Tweak spdlog by @robomics in https://github.com/paulsengroup/hictk/pull/286
• Bump libarchive by @robomics in https://github.com/paulsengroup/hictk/pull/289
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/296

Full Changelog: https://github.com/paulsengroup/hictk/compare/v1.0.0...v2.0.0

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Published by robomics over 1 year ago

hictk - v1.0.0

What's Changed

• Fix incorrect overload being called when fetching pixels from cooler files by @robomics in https://github.com/paulsengroup/hictk/pull/158
• Properly deal with .hic files with missing normalization vectors by @robomics in https://github.com/paulsengroup/hictk/pull/162
• Fix fuzzy tests by @robomics in https://github.com/paulsengroup/hictk/pull/165
• hictk balance: add --no-create-weight-link option by @robomics in https://github.com/paulsengroup/hictk/pull/167
• hictk balance: honor --in-memory by @robomics in https://github.com/paulsengroup/hictk/pull/166
• Add more benchmarks by @robomics in https://github.com/paulsengroup/hictk/pull/164
• Throw an error when a non-existing folder is passed to --tmpdir by @robomics in https://github.com/paulsengroup/hictk/pull/168
• Switch from conanfile.txt to conanfile.py by @robomics in https://github.com/paulsengroup/hictk/pull/169
• Update Docker images used by CI by @robomics in https://github.com/paulsengroup/hictk/pull/173
• Refactor code to return interactions as sparse/dense Eigen matrices by @robomics in https://github.com/paulsengroup/hictk/pull/176
• Fix typo by @Phlya in https://github.com/paulsengroup/hictk/pull/177
• Support fetching interactions as arrow::Table by @robomics in https://github.com/paulsengroup/hictk/pull/170
• For the time being, refuse to build on big-endian architectures by @robomics in https://github.com/paulsengroup/hictk/pull/181
• Support for fetching interactions from the lower triangle when it makes sense by @robomics in https://github.com/paulsengroup/hictk/pull/179
• Drop unnecessary dependency from conanfile.py by @robomics in https://github.com/paulsengroup/hictk/pull/184
• Ensure pixel transformers are well-behaved when given an empty range of pixels by @robomics in https://github.com/paulsengroup/hictk/pull/182
• Support opening .hic files with only 1 bin per chromosome by @robomics in https://github.com/paulsengroup/hictk/pull/180
• Fix typo in conanfile.py by @robomics in https://github.com/paulsengroup/hictk/pull/186
• Update docs by @robomics in https://github.com/paulsengroup/hictk/pull/183
• Various fixes to the build system by @robomics in https://github.com/paulsengroup/hictk/pull/187
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/189

New Contributors

• @Phlya made their first contribution in https://github.com/paulsengroup/hictk/pull/177

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.12...v1.0.0

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Published by robomics almost 2 years ago

hictk - v0.0.12

What's Changed

• Properly support aggregating .scool with float counts by @robomics in https://github.com/paulsengroup/hictk/pull/145
• Install missing targets by @robomics in https://github.com/paulsengroup/hictk/pull/146
• Fix segfault when computing the expected value vector by @robomics in https://github.com/paulsengroup/hictk/pull/147
• Support chained calls to BinTable.subset() by @robomics in https://github.com/paulsengroup/hictk/pull/148
• Drop macOS 11 from CI by @robomics in https://github.com/paulsengroup/hictk/pull/149
• Minor updates to the build system by @robomics in https://github.com/paulsengroup/hictk/pull/150
• Gracefully deal with files created on Win and read on *NIX by @robomics in https://github.com/paulsengroup/hictk/pull/151
• Improve handling of temporary files by @robomics in https://github.com/paulsengroup/hictk/pull/152
• Format project by @robomics in https://github.com/paulsengroup/hictk/pull/153
• Bugfix: query mirroring by @robomics in https://github.com/paulsengroup/hictk/pull/154
• Bump deps by @robomics in https://github.com/paulsengroup/hictk/pull/155
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/156

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.11...v0.0.12

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Published by robomics about 2 years ago

hictk - V0.0.11

What's Changed

• Fix fuzzy tests by @robomics in https://github.com/paulsengroup/hictk/pull/132
• Update docs by @robomics in https://github.com/paulsengroup/hictk/pull/137
• Update CI by @robomics in https://github.com/paulsengroup/hictk/pull/138
• Bump deps by @robomics in https://github.com/paulsengroup/hictk/pull/136
• Address static-analysis warnings by @robomics in https://github.com/paulsengroup/hictk/pull/139
• Improve performance of hictk zoomify when processing .hic files by @robomics in https://github.com/paulsengroup/hictk/pull/133
• Implement hictk dump -t weights by @robomics in https://github.com/paulsengroup/hictk/pull/140
• Add tutorials to the docs by @robomics in https://github.com/paulsengroup/hictk/pull/141
• Implement SCALE and VC balancing by @robomics in https://github.com/paulsengroup/hictk/pull/134
• Refactor by @robomics in https://github.com/paulsengroup/hictk/pull/142

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.10...v0.0.11

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Published by robomics about 2 years ago

hictk - v0.0.10

What's Changed

• Fix fuzzy tests by @robomics in https://github.com/paulsengroup/hictk/pull/121
• Fix build-dockerfile CI by @robomics in https://github.com/paulsengroup/hictk/pull/130
• Make hictk zoomify honor --no-copy-base-resolution when zoomifying .hic files by @robomics in https://github.com/paulsengroup/hictk/pull/129
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/131

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.9...v0.0.10

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Published by robomics about 2 years ago

hictk - v0.0.9

What's Changed

• Remove xxhash leftovers by @robomics in https://github.com/paulsengroup/hictk/pull/113
• Fix hictk dump -t bins for files in .scool format by @robomics in https://github.com/paulsengroup/hictk/pull/114
• Expose .hic file attributes by @robomics in https://github.com/paulsengroup/hictk/pull/115
• Add missing calls to find_dependency to Install.cmake by @robomics in https://github.com/paulsengroup/hictk/pull/116
• Address compiler warnings when compiling with MSVC by @robomics in https://github.com/paulsengroup/hictk/pull/117
• Bump dependencies by @robomics in https://github.com/paulsengroup/hictk/pull/118
• Make hictk load honor the value passed through --assembly by @robomics in https://github.com/paulsengroup/hictk/pull/119
• Initial implementation of a generic multi-res file handle by @robomics in https://github.com/paulsengroup/hictk/pull/120
• Update CI by @robomics in https://github.com/paulsengroup/hictk/pull/122
• Fix CI to build docker image by @robomics in https://github.com/paulsengroup/hictk/pull/123
• Rename bin_size() to resolution() to make API more consistent by @robomics in https://github.com/paulsengroup/hictk/pull/124
• Add links to hictk's publication by @robomics in https://github.com/paulsengroup/hictk/pull/125
• Update docs by @robomics in https://github.com/paulsengroup/hictk/pull/126, https://github.com/paulsengroup/hictk/pull/127
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/128

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.8...v0.0.9

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Published by robomics over 2 years ago

hictk - v0.0.8

What's Changed

• Add --skip-all-vs-all flag to hictk by @robomics in https://github.com/paulsengroup/hictk/pull/108
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/109

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.7...v0.0.8

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Published by robomics over 2 years ago

hictk - v0.0.7

What's Changed

• Bump actions/cache from 3 to 4 by @dependabot in https://github.com/paulsengroup/hictk/pull/103
• Add native support to write .hic files by @robomics in https://github.com/paulsengroup/hictk/pull/102
• Fix integer overflow that could occur when writing .cool files by @robomics in https://github.com/paulsengroup/hictk/pull/104
• Update tests by @robomics in https://github.com/paulsengroup/hictk/pull/105
• Bump dependencies by @robomics in https://github.com/paulsengroup/hictk/pull/106
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/107

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.6...v0.0.7

- C++
Published by robomics over 2 years ago

hictk - v0.0.6

What's Changed

• Fix bug when fetching trans interactions from .hic files by @robomics in https://github.com/paulsengroup/hictk/pull/97
• Fix bug when dumping expected .hic matrices by @robomics in https://github.com/paulsengroup/hictk/pull/98
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/99

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.5...v0.0.6

- C++
Published by robomics over 2 years ago

hictk - v0.0.5

What's Changed

• Bump dependencies by @robomics in https://github.com/paulsengroup/hictk/pull/94
• Fix performance regression in hictk::balance by @robomics in https://github.com/paulsengroup/hictk/pull/95
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/96

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.4...v0.0.5

- C++
Published by robomics over 2 years ago

hictk - v0.0.4

What's Changed

• [bugfix] hictk convert (cool2hic) by @robomics in https://github.com/paulsengroup/hictk/pull/74
• Bump actions/github-script from 6 to 7 by @dependabot in https://github.com/paulsengroup/hictk/pull/75
• Fix typo in weight name to weight type mappings by @robomics in https://github.com/paulsengroup/hictk/pull/76
• Refactor internal::PixelMerger by @robomics in https://github.com/paulsengroup/hictk/pull/78
• Bump dependencies by @robomics in https://github.com/paulsengroup/hictk/pull/80
• Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/paulsengroup/hictk/pull/82
• Update compilers used by CI by @robomics in https://github.com/paulsengroup/hictk/pull/83
• Fix Dockerfile ARM builds by @robomics in https://github.com/paulsengroup/hictk/pull/84
• Add --cis-only and --trans-only CLI options to hictk dump by @robomics in https://github.com/paulsengroup/hictk/pull/79
• Fix CI by @robomics in https://github.com/paulsengroup/hictk/pull/86
• Bump actions/upload-artifact from 3 to 4 by @dependabot in https://github.com/paulsengroup/hictk/pull/88
• Bump actions/download-artifact from 3 to 4 by @dependabot in https://github.com/paulsengroup/hictk/pull/89
• Support variable bin sizes by @robomics in https://github.com/paulsengroup/hictk/pull/81
• Initial implementation of utilities to rename chromosomes in cooler files by @robomics in https://github.com/paulsengroup/hictk/pull/77
• Address clang tidy warnings by @robomics in https://github.com/paulsengroup/hictk/pull/87
• Fix GCC 10 builds by @robomics in https://github.com/paulsengroup/hictk/pull/90
• Update CLI reference docs by @robomics in https://github.com/paulsengroup/hictk/pull/92
• Improve ICE balancing by @robomics in https://github.com/paulsengroup/hictk/pull/93
• Prepare for release by @robomics in https://github.com/paulsengroup/hictk/pull/91

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.3...v0.0.4

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Published by robomics over 2 years ago

hictk - v0.0.3

What's Changed

• Update conanfile.txt by @robomics in https://github.com/paulsengroup/hictk/pull/53
• Support reading hic v6 and v7 by @robomics in https://github.com/paulsengroup/hictk/pull/52
• Improve performance of hictk validate when processing .mcool files by @robomics in https://github.com/paulsengroup/hictk/pull/56
• Update CI by @robomics in https://github.com/paulsengroup/hictk/pull/63, https://github.com/paulsengroup/hictk/pull/64
• Build arm64 Docker images by @robomics in https://github.com/paulsengroup/hictk/pull/65
• Update hictk dump to support dumping resolutions, cells and normalizations by @robomics in https://github.com/paulsengroup/hictk/pull/62
• Improve hictk zoomify by @robomics in https://github.com/paulsengroup/hictk/pull/66
• Update build-dockerfile workflow to test image after build by @robomics in https://github.com/paulsengroup/hictk/pull/67
• Implement ICE balancing by @robomics in https://github.com/paulsengroup/hictk/pull/11
• Implement hictk fix-mcool by @robomics in https://github.com/paulsengroup/hictk/pull/68
• Add docs by @robomics in https://github.com/paulsengroup/hictk/pull/69
• Update README and docs by @robomics in https://github.com/paulsengroup/hictk/pull/71
• Fix segfault by @robomics in https://github.com/paulsengroup/hictk/pull/72
• Prepare for v0.0.3 by @robomics in https://github.com/paulsengroup/hictk/pull/73

New Contributors

• @dependabot made their first contribution in https://github.com/paulsengroup/hictk/pull/55

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.2...v0.0.3

- C++
Published by robomics over 2 years ago

hictk - v0.0.2

What's Changed

• Reduce memory usage when reading .hic8 files by @robomics in https://github.com/paulsengroup/hictk/pull/49
• Improve performance when reading hic files by @robomics in https://github.com/paulsengroup/hictk/pull/50

Full Changelog: https://github.com/paulsengroup/hictk/compare/v0.0.1...v0.0.2

- C++
Published by robomics almost 3 years ago

hictk - v0.0.1

- C++
Published by robomics almost 3 years ago